We demonstrate a size sensitive experimental scheme which enables bidirectional transport and fractionation of paramagnetic colloids in a fluid medium. It is shown that two types of magnetic colloidal particles with different sizes can be simultaneously transported in opposite directions, when deposited above a stripe-patterned ferrite garnet film subjected to a square-wave magnetic modulation. Due to their different sizes, the particles are located at distinct elevations above the surface, and they experience two different energy landscapes, generated by the modulated magnetic substrate. By combining theoretical arguments and numerical simulations, we reveal such energy landscapes, which fully explain the bidirectional transport mechanism. The proposed technique does not require pre-imposed channel geometries such as in conventional microfluidics or lab-on-a-chip systems, and permits remote control over the particle motion, speed and trajectory, by using relatively low intense magnetic fields.